The purpose of this model is to understand how genetic architectures of alternative reproductive tactics impact their maintenance in populations. I’m using an individual-based simulation model with different selection scenarios, types of alternative tactics, and genetic architectures (genome-wide additive genetic variance, supergenes, expression networks).

Overview of the model

Males can be courters or not-courters and parents or not-parents. When the model is run with both traits, this results in four possible morphs: courter/parent, courter/not-parent, not-courter/parent, and not-courter/not-parent. Generations are non-overlapping and there is one reproductive bout per generation. In each generation, the population follows the following timeline:

1. Choosing a nest

A female samples 50 males and chooses a male to nest with based on his courtship trait. If there are no courtship traits in the model, she chooses based on the male’s parental trait. If she does not encouter an acceptable male, she does not nest. If she encounters multiple equally-acceptable males, she randomly selects one of them.

2. Fertilization

Once a female decides to nest, up to three males can fertilize the nest. Courters and parental males can contribute more sperm than non-courter and non-parental males: \(r_{courter}=r_{parent}=8\) and \(r_{non-courter}=r_{non-parent}=4\). A courter/non-parent has \(r_{non-parent}\) and a non-courter/parent has \(r_{parent}\). The male with whom the female is nesting gets \(r_{parent}/\Sigma{n_{sperm}}\) and additional non-parental males (up to 2) get \((r_{non-parent}*0.5/\Sigma{n_{sperm}})\), where \(\Sigma{n_{sperm}}\) is the total number of sperm contributed by all of the males, weighted by the sperm competition factor (0.5 is the default for all males except the nesting male). So, when a female mates with one courter and two non-parentals, \(\Sigma{n_{sperm}}\) = \(r_{courter}\) + 2\(*\)(0.5\(*\)\(r_{sneaker}\)), where \(r_{courter}\) = 8 and \(r_{sneaker}\) = 4, therefore \(\Sigma{n_{sperm}}\) = 12.

That being said, every time a male mates he uses his sperm, so after one mating where a courter fertilizes 50% of the female’s 4 eggs, he only has 6 sperm for his next mating.

3. Nest Survival

Before the babies can survive, the nest has to survive. This step is only relevant when parental traits are in the model - if only the courtship trait is specified, then all progeny in the nest survive at this point. When males have the parental trait, if the female has given eggs to a non-parental male (because she chose based on courtship traits), then the nest has a 10% chance of surviving. If the female has given eggs to a parental male, the nest has a 90% chance of surviving.

4. Density-dependent survival

Once the identities of the surviving nests are known–along with the identities of the parents, including sneaker parents–the offspring are created in the simulation. The offspring are created to fill the full carrying capacity of the population, with the numbers per nest being equally divided among all surviving offspring. This allows the population to maintain a constant population size (prior to viability selection) while maintaining the relative successes of the given genotypes/morphs.

5. Viability selection

Before becoming adults, the offspring experience viability selection. Courters and parental males are disfavored in viability selection, with a survival probability of 0.9950125. If an individual is both a courter and a parental male, the survival probability is 0.9900498. Non-courters and non-parental males have survival probabilities of 1.

Evaluating equilibrium

After 10000 generations, I begin tracking the change in frequency of the courter and parent traits, and do so for 2000 additional generations. I calculate the variance in the change in frequency over those 2000 generations. I declare an equilibrium (‘stasis’) has been reached if the last change in frequency of both traits is less than the variance in changes in frequency.

Unlinked additive genetic variance

In these cases, the traits are encoded by a number (50) of loci, whose alleles contribute additively to determine the trait value. These alleles are all freely recombining and are not adhered to any physical genomic location (aka this is a classical quantitative genetics approach). The overall trait value is compared to a population-level threshold (which is static, in these cases), and if the trait value is above the threshold the male takes the parent or courter morph and if it is below he does not. Below, I’m showing the results from 10 replicates of each scenario.

Courter trait

Females choose nests based on whether the male is a courter or not, and they all prefer courters all of the time (the female preference does not have a genetic basis and does not evolve). The only way that non-courters produce offspring is through sneaking, but all males can be sneakers (both courters and non-courters). Because parental care is not incorporated in this model, all nests survive.

Frequency of the courter morph (each color represents a different replicate)

Frequency of the courter morph (each color represents a different replicate)

Of the 20 replicates, 0 reached an equilibrium by 10000 generations.

Frequency of courters in final generation
CourterFreq CourterW NonCourterW
courter_unlinked_1_summary.txt_1 1 2.00401 0
courter_unlinked_1_summary.txt_2 1 2.08333 0
courter_unlinked_1_summary.txt_3 1 2.11416 0
courter_unlinked_1_summary.txt_4 1 1.97628 0
courter_unlinked_2_summary.txt_1 1 2.00401 0
courter_unlinked_2_summary.txt_2 1 2.08333 0
courter_unlinked_2_summary.txt_3 1 2.11416 0
courter_unlinked_2_summary.txt_4 1 1.97628 0
courter_unlinked_3_summary.txt_1 1 1.94175 0
courter_unlinked_3_summary.txt_2 1 2.02840 0
courter_unlinked_3_summary.txt_3 1 2.10526 0
courter_unlinked_3_summary.txt_4 1 1.98413 0
courter_unlinked_4_summary.txt_1 1 1.94175 0
courter_unlinked_4_summary.txt_2 1 2.02840 0
courter_unlinked_4_summary.txt_3 1 2.10526 0
courter_unlinked_4_summary.txt_4 1 1.98413 0
courter_unlinked_5_summary.txt_1 1 1.93050 0
courter_unlinked_5_summary.txt_2 1 2.00401 0
courter_unlinked_5_summary.txt_3 1 1.93424 0
courter_unlinked_5_summary.txt_4 1 2.00000 0

Parental trait

All females nest with parental males, so the only way non-parental males reproduce is through sneaking. Parental males provide care that allows nests to have a 90% chance of survival. The female preference does not have a genetic basis and does not evolve.

Frequency of parent morph (each color represents a different replicate)

Frequency of parent morph (each color represents a different replicate)

Frequency of parents in final generation
ParentFreq ParentW NonParentW
parent_unlinked_1_summary.txt_1 0.514170 1.35573 0.348548
parent_unlinked_1_summary.txt_2 0.551257 1.44912 0.370690
parent_unlinked_1_summary.txt_3 0.532803 1.39179 0.344681
parent_unlinked_1_summary.txt_4 0.491429 1.37209 0.318352
parent_unlinked_2_summary.txt_1 0.514170 1.35573 0.348548
parent_unlinked_2_summary.txt_2 0.551257 1.44912 0.370690
parent_unlinked_2_summary.txt_3 0.532803 1.39179 0.344681
parent_unlinked_2_summary.txt_4 0.491429 1.37209 0.318352
parent_unlinked_3_summary.txt_1 0.552632 1.36264 0.312217
parent_unlinked_3_summary.txt_2 0.599589 1.49315 0.307692
parent_unlinked_3_summary.txt_3 0.566390 1.39927 0.282297
parent_unlinked_3_summary.txt_4 0.632609 1.75601 0.449704
parent_unlinked_4_summary.txt_1 0.552632 1.36264 0.312217
parent_unlinked_4_summary.txt_2 0.599589 1.49315 0.307692
parent_unlinked_4_summary.txt_3 0.566390 1.39927 0.282297
parent_unlinked_4_summary.txt_4 0.632609 1.75601 0.449704
parent_unlinked_5_summary.txt_1 0.548807 1.62451 0.504808
parent_unlinked_5_summary.txt_2 0.512195 1.60714 0.279167
parent_unlinked_5_summary.txt_3 0.646939 1.66246 0.404624
parent_unlinked_5_summary.txt_4 0.537223 1.25468 0.395652

Variation was maintained in 20 of the 20. 0 of the 20 populations crashed, though. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.

Courtship and Parental Traits

Females choose nests based on males’ courtship trait (they all only nest with courting males, and the female preference does not have a genetic basis and does not evolve), and then the survival of the nest depends on whether the courting male is also a parental male. If the chosen male is a parental male, the nest has a 90% chance of survival. Otherwise, it only has a 10% chance. Non-courters only reproduce through sneaking.

The different runs have different outcomes.

Let’s look at the morph frequencies.

Frequency of the 4 morphs in each rep

Frequency of the 4 morphs in each rep

In some of the runs the population crashed after few generations. This is obvious when looking at the the final frequencies in a table as well:

Frequency of morphs in final generation
Generation Pop PopSize NumMal NumFem NumProgeny ParentThresh ParentFreq ParentW NonParentW CourterThresh CourterFreq CourterW NonCourterW FreqNcNp FreqCNp FreqNcP FreqCP PrefThresh PrefFreq
parent-courter_unlinked_1_summary.txt_1 11999 Pop0 997 492 505 1000 -0.0974451 0.930894 1.83188 1.705880 0.270693 0.930894 1.831880 1.70588 0.0691057 0.000000 0.000000 0.930894 NA NA
parent-courter_unlinked_1_summary.txt_2 11999 Pop1 967 461 506 1000 -0.0974451 0.911063 1.95238 1.512200 0.270693 0.911063 1.952380 1.51220 0.0889371 0.000000 0.000000 0.911063 NA NA
parent-courter_unlinked_1_summary.txt_3 11999 Pop2 946 498 448 1000 -0.0974451 0.905622 1.86475 1.297870 0.270693 0.905622 1.864750 1.29787 0.0943775 0.000000 0.000000 0.905622 NA NA
parent-courter_unlinked_1_summary.txt_4 11999 Pop3 963 463 500 1000 -0.0974451 0.902808 2.01675 1.377780 0.270693 0.902808 2.016750 1.37778 0.0971922 0.000000 0.000000 0.902808 NA NA
parent-courter_unlinked_2_summary.txt_1 11999 Pop0 997 492 505 1000 -0.0974451 0.930894 1.83188 1.705880 0.270693 0.930894 1.831880 1.70588 0.0691057 0.000000 0.000000 0.930894 NA NA
parent-courter_unlinked_2_summary.txt_2 11999 Pop1 967 461 506 1000 -0.0974451 0.911063 1.95238 1.512200 0.270693 0.911063 1.952380 1.51220 0.0889371 0.000000 0.000000 0.911063 NA NA
parent-courter_unlinked_2_summary.txt_3 11999 Pop2 946 498 448 1000 -0.0974451 0.905622 1.86475 1.297870 0.270693 0.905622 1.864750 1.29787 0.0943775 0.000000 0.000000 0.905622 NA NA
parent-courter_unlinked_2_summary.txt_4 11999 Pop3 963 463 500 1000 -0.0974451 0.902808 2.01675 1.377780 0.270693 0.902808 2.016750 1.37778 0.0971922 0.000000 0.000000 0.902808 NA NA
parent-courter_unlinked_3_summary.txt_1 11999 Pop0 955 472 483 1000 0.6239620 0.957627 1.90708 2.350000 -1.050790 0.957627 1.907080 2.35000 0.0423729 0.000000 0.000000 0.957627 NA NA
parent-courter_unlinked_3_summary.txt_2 11999 Pop1 949 473 476 1000 0.6239620 0.942918 1.90135 1.814810 -1.050790 0.942918 1.901350 1.81481 0.0570825 0.000000 0.000000 0.942918 NA NA
parent-courter_unlinked_3_summary.txt_3 11999 Pop2 948 489 459 1000 0.6239620 0.926380 1.84989 1.583330 -1.050790 0.926380 1.849890 1.58333 0.0736196 0.000000 0.000000 0.926380 NA NA
parent-courter_unlinked_3_summary.txt_4 11999 Pop3 952 490 462 1000 0.6239620 0.944898 1.79698 1.962960 -1.050790 0.944898 1.796980 1.96296 0.0551020 0.000000 0.000000 0.944898 NA NA
parent-courter_unlinked_4_summary.txt_1 11999 Pop0 955 472 483 1000 0.6239620 0.957627 1.90708 2.350000 -1.050790 0.957627 1.907080 2.35000 0.0423729 0.000000 0.000000 0.957627 NA NA
parent-courter_unlinked_4_summary.txt_2 11999 Pop1 949 473 476 1000 0.6239620 0.942918 1.90135 1.814810 -1.050790 0.942918 1.901350 1.81481 0.0570825 0.000000 0.000000 0.942918 NA NA
parent-courter_unlinked_4_summary.txt_3 11999 Pop2 948 489 459 1000 0.6239620 0.926380 1.84989 1.583330 -1.050790 0.926380 1.849890 1.58333 0.0736196 0.000000 0.000000 0.926380 NA NA
parent-courter_unlinked_4_summary.txt_4 11999 Pop3 952 490 462 1000 0.6239620 0.944898 1.79698 1.962960 -1.050790 0.944898 1.796980 1.96296 0.0551020 0.000000 0.000000 0.944898 NA NA
parent-courter_unlinked_5_summary.txt_1 11999 Pop0 552 242 310 576 -0.7776460 0.404959 0.00000 0.513889 -0.207521 0.595041 0.513889 0.00000 0.0000000 0.595041 0.404959 0.000000 NA NA
parent-courter_unlinked_5_summary.txt_2 11999 Pop1 753 360 393 832 -0.7776460 0.422222 0.00000 0.355769 -0.207521 0.577778 0.357488 0.00000 0.0000000 0.577778 0.422222 0.000000 NA NA
parent-courter_unlinked_5_summary.txt_3 11999 Pop2 771 382 389 942 -0.7776460 0.382199 0.00000 0.330508 -0.207521 0.617801 0.330508 0.00000 0.0000000 0.617801 0.382199 0.000000 NA NA
parent-courter_unlinked_5_summary.txt_4 11999 Pop3 802 382 420 913 -0.7776460 0.400524 0.00000 0.327511 -0.207521 0.599476 0.327511 0.00000 0.0000000 0.599476 0.400524 0.000000 NA NA

Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter. However, 0 of those reps with variation actually crashed.

Linked additive genetic variance

Courter trait

Frequency of the courter morph with linked QTLs (each color represents a different replicate)

Frequency of the courter morph with linked QTLs (each color represents a different replicate)

Of the 20 replicates, 0 reached an equilibrium by 10000 generations.

Frequency of courters with linked QTLs in final generation
CourterFreq CourterW NonCourterW
courter_linked_1_summary.txt_1 1 1.94175 0
courter_linked_1_summary.txt_2 1 1.98020 0
courter_linked_1_summary.txt_3 1 1.98807 0
courter_linked_1_summary.txt_4 1 2.15983 0
courter_linked_2_summary.txt_1 1 1.94175 0
courter_linked_2_summary.txt_2 1 1.98020 0
courter_linked_2_summary.txt_3 1 1.98807 0
courter_linked_2_summary.txt_4 1 2.15983 0
courter_linked_3_summary.txt_1 1 2.10970 0
courter_linked_3_summary.txt_2 1 1.94553 0
courter_linked_3_summary.txt_3 1 1.96850 0
courter_linked_3_summary.txt_4 1 1.98807 0
courter_linked_4_summary.txt_1 1 2.09644 0
courter_linked_4_summary.txt_2 1 2.00401 0
courter_linked_4_summary.txt_3 1 1.96850 0
courter_linked_4_summary.txt_4 1 2.12314 0
courter_linked_5_summary.txt_1 1 1.89394 0
courter_linked_5_summary.txt_2 1 2.06186 0
courter_linked_5_summary.txt_3 1 1.96850 0
courter_linked_5_summary.txt_4 1 1.98020 0

Every rep has the courtship trait go to fixation.

Parental trait

All females nest with parental males, so the only way non-parental males reproduce is through sneaking. Parental males provide care that allows nests to have a 90% chance of survival. The female preference does not have a genetic basis and does not evolve.

Frequency of parent morph with linked QTLs (each color represents a different replicate)

Frequency of parent morph with linked QTLs (each color represents a different replicate)

Frequency of parents with linked QTLs in final generation
ParentFreq ParentW NonParentW
parent_linked_1_summary.txt_1 0.821782 1.64337 0.677778
parent_linked_1_summary.txt_2 0.834356 1.64706 0.765432
parent_linked_1_summary.txt_3 0.864271 1.63279 0.779412
parent_linked_1_summary.txt_4 0.851272 1.57471 0.960526
parent_linked_2_summary.txt_1 0.821782 1.64337 0.677778
parent_linked_2_summary.txt_2 0.834356 1.64706 0.765432
parent_linked_2_summary.txt_3 0.864271 1.63279 0.779412
parent_linked_2_summary.txt_4 0.851272 1.57471 0.960526
parent_linked_3_summary.txt_1 0.885375 1.60268 0.948276
parent_linked_3_summary.txt_2 0.889535 1.63834 0.719298
parent_linked_3_summary.txt_3 0.871287 1.67955 0.923077
parent_linked_3_summary.txt_4 0.876268 1.72454 0.508197
parent_linked_4_summary.txt_1 0.813820 1.57547 0.721649
parent_linked_4_summary.txt_2 0.809346 1.44804 0.617647
parent_linked_4_summary.txt_3 0.793233 1.56161 0.372727
parent_linked_4_summary.txt_4 0.796992 1.52123 0.592593
parent_linked_5_summary.txt_1 0.897590 1.62640 1.058820
parent_linked_5_summary.txt_2 0.851190 1.67133 0.506667
parent_linked_5_summary.txt_3 0.869478 1.66282 0.630769
parent_linked_5_summary.txt_4 0.847251 1.64904 0.706667

Variation was maintained in 20 of the 20. 0 of the 20 populations crashed, though. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.

Courtship and Parental Traits

Females choose nests based on males’ courtship trait (they all only nest with courting males, and the female preference does not have a genetic basis and does not evolve), and then the survival of the nest depends on whether the courting male is also a parental male. If the chosen male is a parental male, the nest has a 90% chance of survival. Otherwise, it only has a 10% chance. Non-courters only reproduce through sneaking.

Frequency of the two morphs with linked QTLs (courter = green, parent = blue)

Frequency of the two morphs with linked QTLs (courter = green, parent = blue)

The different runs have different outcomes.

Let’s look at the morph frequencies.

Frequency of the 4 morphs in each rep with linked QTLs

Frequency of the 4 morphs in each rep with linked QTLs

In some of the runs the population crashed after few generations. This is obvious when looking at the the final frequencies in a table as well:

Frequency of morphs in final generation (linked loci)
Generation Pop PopSize NumMal NumFem NumProgeny ParentThresh ParentFreq ParentW NonParentW CourterThresh CourterFreq CourterW NonCourterW FreqNcNp FreqCNp FreqNcP FreqCP PrefThresh PrefFreq
parent-courter_linked_1_summary.txt_1 11999 Pop0 976 497 479 1000 0.0955683 0.891348 1.8149000 1.148150 0.136879 0.909457 1.807520 1.0888900 0.0804829 0.0281690 0.0100604 0.8812880 NA NA
parent-courter_linked_1_summary.txt_2 11999 Pop1 1000 494 506 1000 0.0955683 0.890688 1.8727300 1.074070 0.136879 0.888664 1.881550 1.0181800 0.0931174 0.0161943 0.0182186 0.8724700 NA NA
parent-courter_linked_1_summary.txt_3 11999 Pop2 986 486 500 1000 0.0955683 0.915638 1.9056200 1.317070 0.136879 0.907407 1.927440 1.1555600 0.0802469 0.0041152 0.0123457 0.9032920 NA NA
parent-courter_linked_1_summary.txt_4 11999 Pop3 980 476 504 1000 0.0955683 0.909664 1.8822200 0.883721 0.136879 0.934874 1.851690 0.9354840 0.0567227 0.0336134 0.0084034 0.9012610 NA NA
parent-courter_linked_2_summary.txt_1 11999 Pop0 964 477 487 1000 -0.9036380 0.400419 0.0104712 0.318182 -1.223350 0.599581 0.325175 0.0000000 0.0020964 0.5974840 0.3983230 0.0020964 NA NA
parent-courter_linked_2_summary.txt_2 11999 Pop1 964 465 499 1000 -0.9036380 0.453763 0.2938390 0.385827 -1.223350 0.576344 0.589552 0.0101523 0.0021505 0.5440860 0.4215050 0.0322581 NA NA
parent-courter_linked_2_summary.txt_3 11999 Pop2 964 461 503 1000 -0.9036380 0.483731 0.2421520 0.449580 -1.223350 0.548807 0.628458 0.0096154 0.0021692 0.5141000 0.4490240 0.0347072 NA NA
parent-courter_linked_2_summary.txt_4 11999 Pop3 963 468 495 1000 -0.9036380 0.416667 0.0000000 0.326007 -1.223350 0.583333 0.326007 0.0000000 0.0000000 0.5833330 0.4166670 0.0000000 NA NA
parent-courter_linked_3_summary.txt_1 11999 Pop0 964 477 487 1000 -0.9036380 0.400419 0.0104712 0.318182 -1.223350 0.599581 0.325175 0.0000000 0.0020964 0.5974840 0.3983230 0.0020964 NA NA
parent-courter_linked_3_summary.txt_2 11999 Pop1 964 465 499 1000 -0.9036380 0.453763 0.2938390 0.385827 -1.223350 0.576344 0.589552 0.0101523 0.0021505 0.5440860 0.4215050 0.0322581 NA NA
parent-courter_linked_3_summary.txt_3 11999 Pop2 964 461 503 1000 -0.9036380 0.483731 0.2421520 0.449580 -1.223350 0.548807 0.628458 0.0096154 0.0021692 0.5141000 0.4490240 0.0347072 NA NA
parent-courter_linked_3_summary.txt_4 11999 Pop3 963 468 495 1000 -0.9036380 0.416667 0.0000000 0.326007 -1.223350 0.583333 0.326007 0.0000000 0.0000000 0.5833330 0.4166670 0.0000000 NA NA
parent-courter_linked_4_summary.txt_1 11999 Pop0 1000 497 503 1000 -1.6687500 0.903421 1.7772800 1.083330 -0.524978 0.911469 1.763800 1.1590900 0.0784708 0.0181087 0.0100604 0.8933600 NA NA
parent-courter_linked_4_summary.txt_2 11999 Pop1 1000 499 501 1000 -1.6687500 0.879760 1.8678800 0.750000 -0.524978 0.887776 1.857790 0.7500000 0.1062120 0.0140281 0.0060120 0.8737470 NA NA
parent-courter_linked_4_summary.txt_3 11999 Pop2 971 506 465 1000 -1.6687500 0.915020 1.7710600 1.581400 -0.524978 0.934783 1.769560 1.5454500 0.0612648 0.0237154 0.0039526 0.9110670 NA NA
parent-courter_linked_4_summary.txt_4 11999 Pop3 991 508 483 1000 -1.6687500 0.899606 1.7855600 1.098040 -0.524978 0.901575 1.801310 0.9400000 0.0826772 0.0177165 0.0157480 0.8838580 NA NA
parent-courter_linked_5_summary.txt_1 11999 Pop0 1000 490 510 1000 0.0631923 0.908163 1.8134800 1.644440 0.592021 0.912245 1.836690 1.3953500 0.0755102 0.0163265 0.0122449 0.8959180 NA NA
parent-courter_linked_5_summary.txt_2 11999 Pop1 1000 505 495 1000 0.0631923 0.942574 1.7542000 1.448280 0.592021 0.940594 1.770530 1.2000000 0.0455446 0.0118812 0.0138614 0.9287130 NA NA
parent-courter_linked_5_summary.txt_3 11999 Pop2 1000 486 514 1000 0.0631923 0.907407 1.8662100 1.400000 0.592021 0.909465 1.891400 1.1363600 0.0740741 0.0185185 0.0164609 0.8909470 NA NA
parent-courter_linked_5_summary.txt_4 11999 Pop3 1000 503 497 1000 0.0631923 0.936382 1.8280300 1.562500 0.592021 0.930417 1.858970 1.1714300 0.0516899 0.0119284 0.0178926 0.9184890 NA NA

Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter. However, 0 of those reps with variation actually crashed.

Supergenes

Courter trait

Frequency of the courter morph with supergenes (each color represents a different replicate)

Frequency of the courter morph with supergenes (each color represents a different replicate)

Of the 20 replicates, 0 reached an equilibrium by 10000 generations.

Frequency of courters with supergenes in final generation
CourterFreq CourterW NonCourterW
courter_supergene_1_summary.txt_1 1 2.00000 0
courter_supergene_1_summary.txt_2 1 1.89394 0
courter_supergene_1_summary.txt_3 1 2.08768 0
courter_supergene_1_summary.txt_4 1 1.99203 0
courter_supergene_2_summary.txt_1 1 2.07039 0
courter_supergene_2_summary.txt_2 1 2.04082 0
courter_supergene_2_summary.txt_3 1 2.03252 0
courter_supergene_2_summary.txt_4 1 2.02840 0
courter_supergene_3_summary.txt_1 1 2.07039 0
courter_supergene_3_summary.txt_2 1 2.04082 0
courter_supergene_3_summary.txt_3 1 2.03252 0
courter_supergene_3_summary.txt_4 1 2.02840 0
courter_supergene_4_summary.txt_1 1 2.03666 0
courter_supergene_4_summary.txt_2 1 2.04082 0
courter_supergene_4_summary.txt_3 1 2.00401 0
courter_supergene_4_summary.txt_4 1 2.13220 0
courter_supergene_5_summary.txt_1 1 1.91205 0
courter_supergene_5_summary.txt_2 1 2.06612 0
courter_supergene_5_summary.txt_3 1 2.00000 0
courter_supergene_5_summary.txt_4 1 2.10970 0

Parental trait

All females nest with parental males, so the only way non-parental males reproduce is through sneaking. Parental males provide care that allows nests to have a 90% chance of survival. The female preference does not have a genetic basis and does not evolve.

Frequency of parent morph with supergenes (each color represents a different replicate)

Frequency of parent morph with supergenes (each color represents a different replicate)

Frequency of parents with supergenes in final generation
ParentFreq ParentW NonParentW
parent_supergene_1_summary.txt_1 0.852227 1.57720 0.616438
parent_supergene_1_summary.txt_2 0.865613 1.70548 0.750000
parent_supergene_1_summary.txt_3 0.852071 1.58796 0.720000
parent_supergene_1_summary.txt_4 0.845545 1.70492 0.500000
parent_supergene_2_summary.txt_1 0.864440 1.67273 0.753623
parent_supergene_2_summary.txt_2 0.870775 1.65753 0.692308
parent_supergene_2_summary.txt_3 0.844864 1.70471 0.702703
parent_supergene_2_summary.txt_4 0.859073 1.60674 0.657534
parent_supergene_3_summary.txt_1 0.796578 1.49403 0.607477
parent_supergene_3_summary.txt_2 0.783890 1.56391 0.545455
parent_supergene_3_summary.txt_3 0.811429 1.63850 0.545455
parent_supergene_3_summary.txt_4 0.785300 1.58621 0.504505
parent_supergene_4_summary.txt_1 0.796578 1.49403 0.607477
parent_supergene_4_summary.txt_2 0.783890 1.56391 0.545455
parent_supergene_4_summary.txt_3 0.811429 1.63850 0.545455
parent_supergene_4_summary.txt_4 0.785300 1.58621 0.504505
parent_supergene_5_summary.txt_1 0.854839 1.57783 0.472222
parent_supergene_5_summary.txt_2 0.852295 1.57143 0.797297
parent_supergene_5_summary.txt_3 0.849206 1.59112 0.618421
parent_supergene_5_summary.txt_4 0.854685 1.54362 0.671053

Variation was maintained in 20 of the 20. 0 of the 20 populations crashed, though. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.

Courtship and Parental Traits

Females choose nests based on males’ courtship trait (they all only nest with courting males, and the female preference does not have a genetic basis and does not evolve), and then the survival of the nest depends on whether the courting male is also a parental male. If the chosen male is a parental male, the nest has a 90% chance of survival. Otherwise, it only has a 10% chance. Non-courters only reproduce through sneaking.

Frequency of the two morphs with linked QTLs (courter = green, parent = blue)

Frequency of the two morphs with linked QTLs (courter = green, parent = blue)

The different runs have different outcomes.

Let’s look at the morph frequencies.

Frequency of the 4 morphs in each rep with supergenes

Frequency of the 4 morphs in each rep with supergenes

In some of the runs the population crashed after few generations. This is obvious when looking at the the final frequencies in a table as well:

Frequency of morphs in final generation (supergenes)
Generation Pop PopSize NumMal NumFem NumProgeny ParentThresh ParentFreq ParentW NonParentW CourterThresh CourterFreq CourterW NonCourterW FreqNcNp FreqCNp FreqNcP FreqCP PrefThresh PrefFreq
parent-courter_supergene_1_summary.txt_1 11999 Pop0 945 471 474 1000 0.4239010 0.940552 1.92099 2.071430 -0.375768 0.940552 1.920990 2.07143 0.0594480 0.0000000 0.000000 0.940552 NA NA
parent-courter_supergene_1_summary.txt_2 11999 Pop1 960 472 488 1000 0.4239010 0.942797 1.92360 1.592590 -0.375768 0.953390 1.920000 1.59091 0.0466102 0.0105932 0.000000 0.942797 NA NA
parent-courter_supergene_1_summary.txt_3 11999 Pop2 949 473 476 1000 0.4239010 0.938689 1.87387 1.448280 -0.375768 0.938689 1.873870 1.44828 0.0613108 0.0000000 0.000000 0.938689 NA NA
parent-courter_supergene_1_summary.txt_4 11999 Pop3 946 461 485 1000 0.4239010 0.891540 2.02433 1.500000 -0.375768 0.895879 2.024210 1.47917 0.1041210 0.0043384 0.000000 0.891540 NA NA
parent-courter_supergene_2_summary.txt_1 11999 Pop0 945 459 486 1000 -0.9251780 0.424837 0.00000 0.352273 1.141060 0.575163 0.352273 0.00000 0.0000000 0.5751630 0.424837 0.000000 NA NA
parent-courter_supergene_2_summary.txt_2 11999 Pop1 963 473 490 1000 -0.9251780 0.408034 0.00000 0.367857 1.141060 0.591966 0.367857 0.00000 0.0000000 0.5919660 0.408034 0.000000 NA NA
parent-courter_supergene_2_summary.txt_3 11999 Pop2 963 468 495 1000 -0.9251780 0.418803 0.00000 0.378676 1.141060 0.581197 0.378676 0.00000 0.0000000 0.5811970 0.418803 0.000000 NA NA
parent-courter_supergene_2_summary.txt_4 11999 Pop3 959 479 480 1000 -0.9251780 0.409186 0.00000 0.233216 1.141060 0.590814 0.233216 0.00000 0.0000000 0.5908140 0.409186 0.000000 NA NA
parent-courter_supergene_3_summary.txt_1 11999 Pop0 939 494 445 1000 -0.0633515 0.919028 1.88987 1.225000 1.499700 0.919028 1.889870 1.22500 0.0809717 0.0000000 0.000000 0.919028 NA NA
parent-courter_supergene_3_summary.txt_2 11999 Pop1 951 485 466 1000 -0.0633515 0.956701 1.78664 2.619050 1.499700 0.956701 1.786640 2.61905 0.0432990 0.0000000 0.000000 0.956701 NA NA
parent-courter_supergene_3_summary.txt_3 11999 Pop2 937 469 468 1000 -0.0633515 0.963753 1.94469 2.588240 1.499700 0.963753 1.944690 2.58824 0.0362473 0.0000000 0.000000 0.963753 NA NA
parent-courter_supergene_3_summary.txt_4 11999 Pop3 938 471 467 1000 -0.0633515 0.940552 1.89391 1.892860 1.499700 0.940552 1.893910 1.89286 0.0594480 0.0000000 0.000000 0.940552 NA NA
parent-courter_supergene_4_summary.txt_1 11999 Pop0 939 494 445 1000 -0.0633515 0.919028 1.88987 1.225000 1.499700 0.919028 1.889870 1.22500 0.0809717 0.0000000 0.000000 0.919028 NA NA
parent-courter_supergene_4_summary.txt_2 11999 Pop1 951 485 466 1000 -0.0633515 0.956701 1.78664 2.619050 1.499700 0.956701 1.786640 2.61905 0.0432990 0.0000000 0.000000 0.956701 NA NA
parent-courter_supergene_4_summary.txt_3 11999 Pop2 937 469 468 1000 -0.0633515 0.963753 1.94469 2.588240 1.499700 0.963753 1.944690 2.58824 0.0362473 0.0000000 0.000000 0.963753 NA NA
parent-courter_supergene_4_summary.txt_4 11999 Pop3 938 471 467 1000 -0.0633515 0.940552 1.89391 1.892860 1.499700 0.940552 1.893910 1.89286 0.0594480 0.0000000 0.000000 0.940552 NA NA
parent-courter_supergene_5_summary.txt_1 11999 Pop0 941 469 472 1000 0.7707220 0.914712 1.95338 1.675000 0.438833 0.914712 1.953380 1.67500 0.0852878 0.0000000 0.000000 0.914712 NA NA
parent-courter_supergene_5_summary.txt_2 11999 Pop1 998 463 535 1000 0.7707220 0.879050 2.01474 1.339290 0.438833 0.879050 2.014740 1.33929 0.1209500 0.0000000 0.000000 0.879050 NA NA
parent-courter_supergene_5_summary.txt_3 11999 Pop2 938 479 459 1000 0.7707220 0.924843 1.91196 1.527780 0.438833 0.924843 1.911960 1.52778 0.0751566 0.0000000 0.000000 0.924843 NA NA
parent-courter_supergene_5_summary.txt_4 11999 Pop3 966 495 471 1000 0.7707220 0.917172 1.83700 1.341460 0.438833 0.917172 1.837000 1.34146 0.0828283 0.0000000 0.000000 0.917172 NA NA

Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter. However, 0 of those reps with variation actually crashed.